My friends and I are currently working one a Tricoptor project. And our original goal is to have an 100Hz update rate( Which we find impossible on AVR later). While tuning PID, we found that our system only maintain an update rate about 30Hz, Which is a little bit not enough.

I'm wondering that, beside using Arduino DUE to gain faster update rate. Will using two Arduino like MEGA+NANO be an option? If so, how should I divide my code to get better performance. Our project currently have five part: receiving control signal( by Serial through wireless ), getting MPU 6050's signal( by I2C), PID calculating and ESC& servo signal output.

Although I think divide the whole process into two Arduino is a workable plan, but I have no clue on which part should I divide, It will be great idea if anyone can give me an suggestion.

There is an Ardu-IMU project which gives you a self-contained solution to manage the IMU and take care of all the complex number crunching required to deal with that. That would give you a known efficient working solution for the most complex part of your project, leaving your main Arduino and whatever sketch you're running on it to just deal with the closed loop control algorithm. You'll need to read up on the Ardu-IMU and see what sort of update frequency it can achieve - your 100 Hz target seems pretty hard to me, but perhaps it's possible; if not, re-check the analysis that told you 100Hz was necessary, because you may have set the requirements harder than they need to be.

I only provide help via the forum - please do not contact me for private consultancy.

Is this even possible? All I know is I can put different calculation to different processor. Can I ignore the structure and divide it by lines?

They are taking the piss because of your piss poor question. No detailes no sensible answer.

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getting MPU 6050's signal( by I2C),

That is your bottle neck use the I2C master libary, this allows you to up the speed of the bus to 400KHz and beyond if your device can take it. You have got pull up resistors on the bus lines haven't you?Forget two processors.

While tuning PID, we found that our system only maintain an update rate about 30Hz, Which is a little bit not enough.

The first rule of performance tuning: find out where the time is spent. Actually this rule is also rules 2,3,4,5,6,7,8,9, etc.Do not guess! Human intuition on computer performance is very unreliable. Measure, measure, measure!

For the Arduino simply have a few long variables, e.g. loopStart, loopMid, LoopWhatever, .,,.Assign loopStart = micros(); and so forth. At the end of the loop print the values (not in the loop!).By this method you will find the actual bottleneck - not somebody's guess.